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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ), 'gf_id' => 'ORTHO05D000948', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ), 'data_identifier' => 'ORTHO05D000948', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000948', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '542', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p44530' => 'bna', 'A04p09950' => 'bna', 'A06p43990' => 'bna', 'A07p11950' => 'bna', 'Aa31LG2G8070' => 'aar', 'Aa31LG7G9880' => 'aar', 'Aa31sc107G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.738' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1622' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1918' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.3654' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2397' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3092' => 'aag', 'Actinidia03615' => 'ach', 'Actinidia08063' => 'ach', 'Actinidia09642' => 'ach', 'Actinidia12436' => 'ach', 'Actinidia20116' => 'ach', 'Actinidia20117' => 'ach', 'Actinidia21441' => 'ach', 'Actinidia30637' => 'ach', 'Ah.01g002560' => 'amhyb', 'Ah.03g136050' => 'amhyb', 'AL1G40720' => 'aly', 'AL5G10950' => 'aly', 'AL7G44620' => 'aly', 'Aqoxy3G04024' => 'aox', 'Aqoxy4G02228' => 'aox', 'Aqoxy5G03326' => 'aox', 'Aqoxy7G04201' => 'aox', 'arahy.Tifrunner.gnm1.ann1.10B7TY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.17357K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8A2QUP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KX9XE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATD06R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYB4A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LSBE5R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7J14L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X8JHA4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XFB661' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y7Y5CU' => 'arhy', 'AT1G27320' => 'ath', 'AT2G01830' => 'ath', 'AT5G35750' => 'ath', 'ATR0561G280' => 'atr', 'ATR0624G062' => 'atr', 'Atru.chr11.2340' => 'acertr', 'Atru.chr11.2341' => 'acertr', 'Atru.chr11.763' => 'acertr', 'Atru.chr11.769' => 'acertr', 'Atru.chr6.3356' => 'acertr', 'AUR62005635' => 'cqu', 'AUR62015027' => 'cqu', 'AUR62028914' => 'cqu', 'AUR62029085' => 'cqu', 'BcaB06g26981' => 'bca', 'BcaC01g03182' => 'bca', 'BcaC02g09497' => 'bca', 'BcaC06g31271' => 'bca', 'BcaC06g34107' => 'bca', 'BcaNung06814' => 'bca', 'BolC3t17805H' => 'bol', 'BolC4t25926H' => 'bol', 'BolC7t42295H' => 'bol', 'BolC7t43785H' => 'bol', 'BraA03t13586Z' => 'bra', 'BraA04t16657Z' => 'bra', 'BraA06t27274Z' => 'bra', 'BraA07t28980Z' => 'bra', 'C03p55330' => 'bna', 'C04p43460' => 'bna', 'C07p17890' => 'bna', 'C07p32560' => 'bna', 'C07p32590' => 'bna', 'C07p32610' => 'bna', 'CAN.G1036.13' => 'can', 'CAN.G240.1' => 'can', 'CAN.G74.29' => 'can', 'CANSAT64G0551' => 'cansat', 'CANSAT78G1921' => 'cansat', 'CARHR026900' => 'chi', 'CARHR144390' => 'chi', 'CARHR216810' => 'chi', 'CARHR292390' => 'chi', 'Carub.0001s2585' => 'cru', 'Carub.0005s0080' => 'cru', 'Carub.0007s3151' => 'cru', 'Ca_06460_v3' => 'car', 'Ca_16450_v3' => 'car', 'Ca_17241_v3' => 'car', 'Ca_18021_v3' => 'car', 'Ca_30369_v3' => 'car', 'CBR_g23952' => 'cbr', 'CBR_g29924' => 'cbr', 'CBR_g29925' => 'cbr', 'CBR_g38370' => 'cbr', 'CBR_g3865' => 'cbr', 'CBR_g4036' => 'cbr', 'CBR_g45573' => 'cbr', 'CBR_g45915' => 'cbr', 'CBR_g45917' => 'cbr', 'CBR_g48213' => 'cbr', 'CBR_g55544' => 'cbr', 'CBR_g57125' => 'cbr', 'CBR_g74916' => 'cbr', 'Cc05_g02360' => 'ccan', 'Cc11_g06260' => 'ccan', 'Cc11_g17030' => 'ccan', 'CDE02G2093' => 'cde', 'CDE02G3601' => 'cde', 'CDE05G1265' => 'cde', 'CDE05G1629' => 'cde', 'CDE05G2353' => 'cde', 'CDE06G2676' => 'cde', 'Cfa009375' => 'cfa', 'Cfa014243' => 'cfa', 'Cfa015059' => 'cfa', 'Cfa023105' => 'cfa', 'Ciclev10014068m.g' => 'ccl', 'Ciclev10014137m.g' => 'ccl', 'Ciclev10030589m.g' => 'ccl', 'CiPaw.03G278600' => 'cil', 'CiPaw.04G196100' => 'cil', 'CiPaw.05G108300' => 'cil', 'CiPaw.05G188200' => 'cil', 'CiPaw.06G009200' => 'cil', 'CiPaw.06G056700' => 'cil', 'CiPaw.06G103900' => 'cil', 'ClCG01G006710' => 'cla', 'ClCG02G002700' => 'cla', 'ClCG02G009380' => 'cla', 'ClCG06G002200' => 'cla', 'ClCG11G001010' => 'cla', 'COL.COLO4_20421' => 'col', 'COL.COLO4_27599' => 'col', 'COL.COLO4_33016' => 'col', 'Cpa.g.sc136.20' => 'cpa', 'Cpa.g.sc2.143' => 'cpa', 'Cpa.g.sc43.73' => 'cpa', 'Cre07.g329900' => 'cre', 'Cre07.g330000' => 'cre', 'Cre13.g571200' => 'cre', 'CsaV3_5G013000' => 'csa', 'CsaV3_5G027850' => 'csa', 'CsaV3_6G008270' => 'csa', 'CsaV3_6G009450' => 'csa', 'CsaV3_UNG033160' => 'csa', 'CSS0011606' => 'camsi', 'CSS0013134' => 'camsi', 'CSS0025462' => 'camsi', 'CSS0027893' => 'camsi', 'CSS0046144' => 'camsi', 'CSS0046207' => 'camsi', 'DCAR_002667' => 'dca', 'DCAR_019705' => 'dca', 'DCAR_023548' => 'dca', 'DCAR_024116' => 'dca', 'DCAR_024678' => 'dca', 'DCAR_026815' => 'dca', 'Dinv05354' => 'din', 'Dinv11678' => 'din', 'Dinv11766' => 'din', 'Dinv14380' => 'din', 'Dinv17573' => 'din', 'Dinv21275' => 'din', 'Duzib133G0898' => 'dzi', 'Duzib138G1724' => 'dzi', 'Duzib248G0484' => 'dzi', 'Duzib248G1570' => 'dzi', 'Duzib251G0585' => 'dzi', 'Duzib251G0681' => 'dzi', 'Duzib268G0709' => 'dzi', 'Duzib268G0719' => 'dzi', 'ECA233G3162' => 'eca', 'ECA233G3277' => 'eca', 'ECA234G1263' => 'eca', 'ECA236G3256' => 'eca', 'EL10Ac6g13521' => 'bvu', 'EL10Ac9g22703' => 'bvu', 'Eucgr.A01042' => 'egr', 'Eucgr.B02664' => 'egr', 'Eucgr.B03506' => 'egr', 'Eucgr.C00012' => 'egr', 'Eucgr.C01148' => 'egr', 'Eucgr.F04315' => 'egr', 'Eucgr.H04628' => 'egr', 'Eucgr.H04632' => 'egr', 'Eucgr.J00801' => 'egr', 'Eucgr.J00805' => 'egr', 'Eucgr.K00060' => 'egr', 'FAN02G2850' => 'fan', 'FAN05G2042' => 'fan', 'FAN07G0202' => 'fan', 'FAN07G0235' => 'fan', 'FAN07G0322' => 'fan', 'FAN09G3350' => 'fan', 'FAN11G2934' => 'fan', 'FAN12G0277' => 'fan', 'FAN12G1470' => 'fan', 'FAN14G3849' => 'fan', 'FAN16G0442' => 'fan', 'FAN17G2312' => 'fan', 'FAN17G2757' => 'fan', 'FAN21G2886' => 'fan', 'FAN22G1098' => 'fan', 'FAN25G2117' => 'fan', 'FvH4_3g03620' => 'fve', 'FvH4_4g23590' => 'fve', 'FvH4_4g33130' => 'fve', 'FvH4_6g41180' => 'fve', 'Glyma.02G087000' => 'gma', 'Glyma.02G305900' => 'gma', 'Glyma.05G148100' => 'gma', 'Glyma.05G241600' => 'gma', 'Glyma.07G158750' => 'gma', 'Glyma.07G158801' => 'gma', 'Glyma.07G173700' => 'gma', 'Glyma.08G049000' => 'gma', 'Glyma.08G105000' => 'gma', 'Glyma.14G007100' => 'gma', 'Gohir.A01G154300' => 'ghi', 'Gohir.A03G112400' => 'ghi', 'Gohir.A03G112450' => 'ghi', 'Gohir.A03G114500' => 'ghi', 'Gohir.A03G119501' => 'ghi', 'Gohir.A07G166800' => 'ghi', 'Gohir.A11G149900' => 'ghi', 'Gohir.A12G149200' => 'ghi', 'Gohir.A12G154200' => 'ghi', 'Gohir.A13G029300' => 'ghi', 'Gohir.D01G146500' => 'ghi', 'Gohir.D02G137000' => 'ghi', 'Gohir.D02G147800' => 'ghi', 'Gohir.D04G055375' => 'ghi', 'Gohir.D07G172100' => 'ghi', 'Gohir.D11G156400' => 'ghi', 'Gohir.D12G153100' => 'ghi', 'Gohir.D12G157400' => 'ghi', 'Gohir.D13G027400' => 'ghi', 'Gohir.D13G027500' => 'ghi', 'Gorai.001G192400' => 'gra', 'Gorai.002G182200' => 'gra', 'Gorai.005G153000' => 'gra', 'Gorai.005G165600' => 'gra', 'Gorai.007G166900' => 'gra', 'Gorai.008G165600' => 'gra', 'Gorai.008G170200' => 'gra', 'Gorai.013G031500' => 'gra', 'GSVIVG01008148001' => 'vvi', 'GSVIVG01010502001' => 'vvi', 'GSVIVG01011612001' => 'vvi', 'GSVIVG01030058001' => 'vvi', 'HanXRQChr08g0209661' => 'han', 'HanXRQChr08g0224601' => 'han', 'HanXRQChr10g0306861' => 'han', 'HanXRQChr12g0361291' => 'han', 'HanXRQChr12g0366181' => 'han', 'HanXRQChr12g0373961' => 'han', 'Haze_09936' => 'cav', 'Haze_10832' => 'cav', 'Haze_12434' => 'cav', 'Haze_12690' => 'cav', 'Hma1.2p1_0037F.1_g023870' => 'hma', 'Hma1.2p1_0065F.1_g035320' => 'hma', 'Hma1.2p1_0545F.1_g176090' => 'hma', 'HPP92_006531' => 'vpl', 'HPP92_006532' => 'vpl', 'HPP92_007963' => 'vpl', 'HPP92_008013' => 'vpl', 'HPP92_011754' => 'vpl', 'HPP92_011755' => 'vpl', 'HPP92_011776' => 'vpl', 'HPP92_023437' => 'vpl', 'Hund01576' => 'sun', 'Hund06098' => 'sun', 'Hund25472' => 'sun', 'Lalb_Chr04g0247261' => 'lal', 'Lalb_Chr04g0258751' => 'lal', 'Lalb_Chr05g0222031' => 'lal', 'Lalb_Chr07g0187061' => 'lal', 'Lalb_Chr08g0230581' => 'lal', 'Lalb_Chr13g0294411' => 'lal', 'Lalb_Chr13g0294481' => 'lal', 'Lalb_Chr13g0294491' => 'lal', 'Lalb_Chr13g0294501' => 'lal', 'Lalb_Chr13g0294521' => 'lal', 'Lalb_Chr16g0387371' => 'lal', 'Lalb_Chr17g0349091' => 'lal', 'Lalb_Chr17g0349101' => 'lal', 'Lj1A793T49' => 'lonja', 'Lj2g0006378' => 'lja', 'Lj2g0019787' => 'lja', 'Lj2g0020718' => 'lja', 'Lj2P928T8' => 'lonja', 'Lj2P943T8' => 'lonja', 'Lj3A1070T23' => 'lonja', 'Lj3A861T62' => 'lonja', 'Lj4g0014583' => 'lja', 'Lj4g0022949' => 'lja', 'Lj4g0024800' => 'lja', 'Lj6A733G59' => 'lonja', 'Lj9A83G54' => 'lonja', 'Lj9A85T82' => 'lonja', 'Lj9C83G8' => 'lonja', 'Lj9C86G1' => 'lonja', 'Lj9P302T42' => 'lonja', 'Lj9P461T45' => 'lonja', 'LjContig00081g0007941' => 'lja', 'LjContig00230g0026897' => 'lja', 'Lju1034C2G7' => 'lonja', 'Lju170C29G5' => 'lonja', 'Lju2000A0T45' => 'lonja', 'Lju225A1T15' => 'lonja', 'Lsat_1_v5_gn_4_23060' => 'lsa', 'Lsat_1_v5_gn_5_121700' => 'lsa', 'Lsat_1_v5_gn_7_95341' => 'lsa', 'Lsat_1_v5_gn_8_147740' => 'lsa', 'Lsat_1_v5_gn_8_36401' => 'lsa', 'Manes.12G009800' => 'mes', 'Manes.12G061600' => 'mes', 'Manes.13G010500' => 'mes', 'Manes.13G063800' => 'mes', 'Manes.15G137400' => 'mes', 'Mapoly0059s0005' => 'mpo', 'Mapoly0063s0029' => 'mpo', 'Mapoly0075s0066' => 'mpo', 'Mapoly0082s0006' => 'mpo', 'Mapoly0104s0036' => 'mpo', 'MBI07_g36564_MAGBIO' => 'mbi', 'MBI11_g41398_MAGBIO' => 'mbi', 'MBI19_g23690_MAGBIO' => 'mbi', 'MBI19_g25588_MAGBIO' => 'mbi', 'MCO04G532' => 'mco', 'MD09G1121900' => 'mdo', 'MD13G1017000' => 'mdo', 'MD13G1120900' => 'mdo', 'MD16G1014900' => 'mdo', 'MD16G1068400' => 'mdo', 'MD16G1120900' => 'mdo', 'MD17G1113000' => 'mdo', 'Medtr2g067240' => 'mtr', 'Medtr3g085130' => 'mtr', 'Medtr5g044100' => 'mtr', 'Medtr5g097410' => 'mtr', 'Medtr8g080770' => 'mtr', 'Medtr8g106150' => 'mtr', 'MELO3C005250.2' => 'cme', 'MELO3C020055.2' => 'cme', 'MELO3C022310.2' => 'cme', 'MELO3C025982.2' => 'cme', 'Migut.E00012' => 'egut', 'Migut.E00529' => 'egut', 'MSTRG.12242' => 'ama', 'MSTRG.13647' => 'ama', 'MSTRG.2107' => 'ama', 'MSTRG.2108' => 'ama', 'MSTRG.8014' => 'ama', 'Nitab4.5_0000996g0050' => 'nta', 'Nitab4.5_0001701g0010' => 'nta', 'Nitab4.5_0001774g0030' => 'nta', 'Nitab4.5_0002951g0010' => 'nta', 'Nitab4.5_0003884g0020' => 'nta', 'Nitab4.5_0011720g0010' => 'nta', 'Nn1g07465' => 'nnu', 'Nn3g16439' => 'nnu', 'Nn4g22290' => 'nnu', 'Nn4g24487' => 'nnu', 'Oeu004458.1' => 'oeu', 'Oeu004459.1' => 'oeu', 'Oeu004460.1' => 'oeu', 'Oeu012346.1' => 'oeu', 'Oeu012347.1' => 'oeu', 'Oeu024857.1' => 'oeu', 'Oeu035474.1' => 'oeu', 'Oeu040466.1' => 'oeu', 'Oeu042910.1' => 'oeu', 'Oeu048819.1' => 'oeu', 'Oeu049143.1' => 'oeu', 'Oeu056666.1' => 'oeu', 'Os01g0923700' => 'osa', 'Os02g0738400' => 'osa', 'Os03g0717700' => 'osa', 'Os10g0362300' => 'osa', 'Os12g0454800' => 'osa', 'Peaxi162Scf00128g01329' => 'pax', 'Peaxi162Scf00337g00622' => 'pax', 'Peaxi162Scf00776g00011' => 'pax', 'PGR102G1193' => 'pgr', 'PGR119G0177' => 'pgr', 'PGR119G2297' => 'pgr', 'PGSC0003DMG400006145' => 'stu', 'PGSC0003DMG400029463' => 'stu', 'PGSC0003DMG400034307' => 'stu', 'Phvul.002G324900' => 'pvu', 'Phvul.003G015500' => 'pvu', 'Phvul.008G285800' => 'pvu', 'Phvul.L002746' => 'pvu', 'Potri.001G057400' => 'ptr', 'Potri.003G171000' => 'ptr', 'Potri.008G137900' => 'ptr', 'Potri.010G102900' => 'ptr', 'Potri.014G164700' => 'ptr', 'Pp3c16_300' => 'ppa', 'Pp3c16_7610' => 'ppa', 'Pp3c17_4020' => 'ppa', 'Pp3c18_4620' => 'ppa', 'Pp3c18_4650' => 'ppa', 'Pp3c1_20050' => 'ppa', 'Pp3c20_17580' => 'ppa', 'Pp3c21_18040' => 'ppa', 'Pp3c22_15240' => 'ppa', 'Pp3c24_10780' => 'ppa', 'Pp3c25_8540' => 'ppa', 'Pp3c2_19330' => 'ppa', 'Pp3c2_20110' => 'ppa', 'Pp3c4_1360' => 'ppa', 'Pp3c5_21420' => 'ppa', 'Pp3c5_9120' => 'ppa', 'Pp3c6_11730' => 'ppa', 'Pp3c6_7030' => 'ppa', 'Pp3c9_18950' => 'ppa', 'Pp3c9_21840' => 'ppa', 'Pp3c9_4870' => 'ppa', 'Prupe.1G224300' => 'ppe', 'Prupe.1G336400' => 'ppe', 'Prupe.3G201700' => 'ppe', 'Psat2g004360' => 'psa', 'Psat5g097280' => 'psa', 'Psat7g004720' => 'psa', 'Psat7g077280' => 'psa', 'PSO017G4578' => 'pso', 'PSO063G5931' => 'pso', 'PSO478G4195' => 'pso', 'PSO675G5505' => 'pso', 'PSO782G2389' => 'pso', 'QL03p038622' => 'qlo', 'QL03p052262' => 'qlo', 'QL08p028699' => 'qlo', 'QL11p005400' => 'qlo', 'RcHm_v2.0_Chr2g0156741' => 'rch', 'RcHm_v2.0_Chr4g0430011' => 'rch', 'RcHm_v2.0_Chr4g0442181' => 'rch', 'Rhsim04G0038000' => 'rsi', 'Rhsim04G0038300' => 'rsi', 'Rhsim09G0086800' => 'rsi', 'Rhsim12G0025000' => 'rsi', 'Rhsim12G0092500' => 'rsi', 'Sabra01G0041600' => 'sbr', 'Sabra03G0125100' => 'sbr', 'Sabra08G0105000' => 'sbr', 'Sabra10G0075500' => 'sbr', 'Sabra14G0125400' => 'sbr', 'Sabra15G0065500' => 'sbr', 'SalBow2G1686' => 'sbo', 'SalBow8G1762' => 'sbo', 'Sc04g0010220' => 'sci', 'Sc14g0006760' => 'sci', 'Sc21g0000660' => 'sci', 'Sc21g0000710' => 'sci', 'Sed0006248' => 'sed', 'Sed0006258' => 'sed', 'Sed0015512' => 'sed', 'Sed0016680' => 'sed', 'Sed0020303' => 'sed', 'Sed0020999' => 'sed', 'Sed0025777' => 'sed', 'SEGI_06327' => 'sgi', 'SEGI_06997' => 'sgi', 'SEGI_07945' => 'sgi', 'SEGI_12692' => 'sgi', 'SEGI_13395' => 'sgi', 'SEGI_22142' => 'sgi', 'SEGI_30340' => 'sgi', 'SEGI_38572' => 'sgi', 'SGA_v2.0_scaffold23G10106' => 'sas', 'SGA_v2.0_scaffold65G22139' => 'sas', 'SGA_v2.0_scaffold87G27162' => 'sas', 'SHI10136' => 'shi', 'SHI10137' => 'shi', 'SMO118G0025' => 'smo', 'SMO143G0077' => 'smo', 'SMO165G0139' => 'smo', 'SMO169G0158' => 'smo', 'SMO230G0074' => 'smo', 'SMO340G0108' => 'smo', 'SMO358G0569' => 'smo', 'SMO367G0515' => 'smo', 'SMO367G0856' => 'smo', 'Solyc04g008110.3' => 'sly', 'Solyc05g015610.3' => 'sly', 'Solyc07g047770.4' => 'sly', 'Sopen04g003250' => 'spe', 'Sopen05g011050' => 'spe', 'Sopen07g024210' => 'spe', 'Sp1g23560' => 'spa', 'Sp2g13260' => 'spa', 'Sp3g23540' => 'spa', 'Sp7g06410' => 'spa', 'Sp7g06420' => 'spa', 'TAR374G0502' => 'tar', 'TAR374G1546' => 'tar', 'TAR622G0541' => 'tar', 'TAR622G1231' => 'tar', 'TAR627G0907' => 'tar', 'TAR629G2377' => 'tar', 'TAR629G2776' => 'tar', 'THA.LOC104805094' => 'tha', 'THA.LOC104815356' => 'tha', 'THA.LOC104822796' => 'tha', 'Thecc.01G190700' => 'tca', 'Thecc.02G205500' => 'tca', 'Thecc.02G305700' => 'tca', 'Thhalv10003542m.g' => 'esa', 'Thhalv10003561m.g' => 'esa', 'Thhalv10006654m.g' => 'esa', 'TPR.G1286' => 'tpr', 'TPR.G12959' => 'tpr', 'TPR.G17770' => 'tpr', 'TWI18G0933' => 'twi', 'TWI18G1312' => 'twi', 'TWI36G0233' => 'twi', 'TWI36G1281' => 'twi', 'TWI79G1359' => 'twi', 'unitig_22.g5521' => 'ugi', 'unitig_27.g25302' => 'ugi', 'unitig_8.g4021' => 'ugi', 'vmacro01054' => 'vma', 'vmacro09401' => 'vma', 'vmacro16102' => 'vma', 'VMungo0251G2047' => 'vmu', 'VMungo0251G3253' => 'vmu', 'VMungo0647G1660' => 'vmu', 'VMungo1215G1890' => 'vmu', 'Zm00001eb055280' => 'zma', 'Zm00001eb143050' => 'zma', 'Zm00001eb181520' => 'zma', 'Zm00001eb190410' => 'zma', 'Zm00001eb216090' => 'zma', 'Zm00001eb224010' => 'zma', 'Zm00001eb253970' => 'zma', 'Zm00001eb364280' => 'zma', 'Zm00001eb432690' => 'zma' ) $gf_id = 'ORTHO05D000948' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000948' ) $data_identifier = 'ORTHO05D000948' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 6, 'ach' => (int) 8, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 4, 'bca' => (int) 6, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 13, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 11, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 20, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 16, 'lja' => (int) 8, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 5, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 5, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 12, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 21, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 8, 'sas' => (int) 3, 'shi' => (int) 2, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb432690' $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